Cell-type-specific DNA methylation analysis of the frontal cortices of mutant Polg1 transgenic mice with neuronal accumulation of deleted mitochondrial DNA

Bipolar disorder (BD) is a severe psychiatric disorder characterized by repeated conflicting manic and depressive states. In addition to genetic factors, complex gene–environment interactions, which alter the epigenetic status in the brain, contribute to the etiology and pathophysiology of BD. Here, we performed a promoter-wide DNA methylation analysis of neurons and nonneurons derived from the frontal cortices of mutant Polg1 transgenic (n = 6) and wild-type mice (n = 6). The mutant mice expressed a proofreading-deficient mitochondrial DNA (mtDNA) polymerase under the neuron-specific CamK2a promoter and showed BD-like behavioral abnormalities, such as activity changes and altered circadian rhythms. We identified a total of 469 differentially methylated regions (DMRs), consisting of 267 neuronal and 202 nonneuronal DMRs. Gene ontology analysis of DMR-associated genes showed that cell cycle-, cell division-, and inhibition of peptide activity-related genes were enriched in neurons, whereas synapse- and GABA-related genes were enriched in nonneurons. Among the DMR-associated genes, Trim2 and Lrpprc showed an inverse relationship between DNA methylation and gene expression status. In addition, we observed that mutant Polg1 transgenic mice shared several features of DNA methylation changes in postmortem brains of patients with BD, such as dominant hypomethylation changes in neurons, which include hypomethylation of the molecular motor gene and altered DNA methylation of synapse-related genes in nonneurons. Taken together, the DMRs identified in this study will contribute to understanding the pathophysiology of BD from an epigenetic perspective.

Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state

ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.

Azo-dye Antibacterial with Nanotube-[SiO2(OH)2]9 System for Drug Delivery Investigation

Azo dye, [SiO2(OH)2]9 molecular ring, and single-walled carbon nanotubes (4,4) SWCNT were considered like an axle, a wheel, and stoppers, respectively. The combination of the azo dye on the [SiO2(OH)2]9 molecular ring with (4,4) SWCNTs may be thought of as a non-covalent system in UV light-isomer- machine. A new molecular motor system that runs like a hinge motion is demonstrated like light-powered molecular hinges. A new molecular motor system that acts as a hinge motion has been demonstrated and introduced as light-moving molecular hinges. By emitting various ultraviolet, visible lights, the [SiO2 (OH)2]9 molecular ring in the system can be reversed with the various dumb-bell size on one side attached halogens and fixing it on the other side of the (4,4) SWCNTs surface, a variety of systems in a wide variety of ultraviolet sensors can be designated to a better model of molecular machines and can be used for drug delivery of some antibiotics that are difficult to administer by straight injection. Molecular machines containing a wide variety of ultraviolet sensors have been designed with the combination of azo derivatives formed by replacing different halogens with hydrogen in the azo dye on the [SiO2(OH)2]9 molecular ring to the (4,4) SWCNTs surface.

The Salmonella effector SifA initiates a kinesin-1 and kinesin-3 recruitment process mirroring that mediated by Arl8a/b

When intracellular, pathogenic Salmonella reside in a membrane compartment composed of interconnected vacuoles and tubules, the formation of which depends on the translocation of bacterial effectors into the host cell. Cytoskeletons and their molecular motors are prime targets for these effectors. In this study, we show that the microtubule molecular motor KIF1Bß, a member of the kinesin-3 family, is a key element for the establishment of the Salmonella replication niche as its absence is detrimental to the stability of bacterial vacuoles and the formation of associated tubules. Kinesin-3 interacts with the Salmonella effector SifA but also with SKIP, a host protein complexed to SifA. The interaction with SifA is essential for the recruitment of kinesin-3 on Salmonella vacuoles while that with SKIP is incidental. In the non-infectious context, however, the interaction with SKIP is essential for the recruitment and activity of kinesin-3 on a part of lysosomes. Finally, our results show that in infected cells, the presence of SifA establishes a kinesin-1 and kinesin-3 recruitment pathway that is analogous to and functions independently of that mediated by the Arl8a/b GTPases.

Investigation of the molecular motor of muscle: from generating life in a test tube to myosin structure over beers

This article traces 60 years of investigation of the molecular motor of skeletal muscle from the 1940s through the 1990s. It started with the discovery that myosin interaction with actin in the presence of ATP caused shortening of threads of actin and myosin. In 1957, structures protruding from myosin filaments were seen for the first time and called “cross bridges.” A combination of techniques led to the proposal in 1969 of the “swinging-tilting cross bridge” model of contraction. In the early 1980s, a major problem arose when it was shown that a probe attached to the cross bridges did not move during contraction. A spectacular breakthrough came when it was discovered that only the cross bridge was required to support movement in an in vitro motility assay. Next it was determined that single myosin molecules caused the movement of actin filaments in 10-nm steps. The atomic structure of the cross bridge was published in 1993, and this discovery supercharged the muscle field. The cross bridge contained a globular head or motor domain that bound actin and ATP. But the most striking feature was the long tail of the cross bridge surrounded by two subunits of the myosin molecule. This structure suggested that the tail might act as a lever arm magnifying head movement. Consistent with this proposal, genetic techniques that lengthened the lever arm resulted in larger myosin steps. Thus the molecular motor of muscle operated not by the tilting of the globular head of myosin but by tilting of the lever arm generating the driving force for contraction.

Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component

Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function. The simplest of rotary motors is the archaellum, a molecular motor that spins a helical propeller for archaeal motility analogous to the bacterial flagellum. Curiously, emergence of archaellar rotation may have pivoted on the simple duplication and repurposing of a pre-existing component to produce a stator complex that anchors to the cell superstructure to enable productive rotation of the rotor component. This putative stator complex is composed of ArlF and ArlG, gene duplications of the filament component ArlB, providing an opportunity to study how gene duplication and neofunctionalization contributed to the radical innovation of rotary function. Toward understanding how this happened, we used electron cryomicroscopy to determine the structure of isolated ArlG filaments, the major component of the stator complex. Using a hybrid modeling approach incorporating structure prediction and validation, we show that ArlG filaments are open helices distinct to the closed helical filaments of ArlB. Curiously, further analysis reveals that ArlG retains a subset of the inter-protomer interactions of homologous ArlB, resulting in a superficially different assembly that nevertheless reflects the common ancestry of the two structures. This relatively simple mechanism to change quaternary structure was likely associated with the evolutionary neofunctionalization of the archaellar stator complex, and we speculate that the relative deformable elasticity of an open helix may facilitate elastic energy storage during the transmission of the discrete bursts of energy released by ATP hydrolysis to continuous archaellar rotation, allowing the inherent properties of a duplicated ArlB to be co-opted to fulfill a new role. Furthermore, agreement of diverse experimental evidence in our work supports recent claims to the power of new structure prediction techniques.

Active mechanical threading by a molecular motor

Molecular motors transform external energy input into directional motions and offer exquisite precision for nano-scale manipulations. In order to make full use of molecular motor capacities, their directional motions need to be transmitted and used for powering downstream molecular events – a current great challenge for molecular engineers. Here we present a macrocyclic molecular motor structure able to perform repetitive molecular threading of a flexible polyethylene glycol chain through the macrocycle. This mechanical threading event is actively powered by the motor motions and leads to a direct translation of the unidirectional motor rotation into an unidirectional translation motion (chain versus ring). The step by step mechanism of the active mechanical threading is elucidated and also the actual threading step is identified as a combined helix inversion and threading event. The here established molecular machine function resembles the crucial step of macroscopic weaving or sewing processes and therefore offers a first entry point for realizing a “molecular knitting” counterpart.

Gliding motility of Plasmodium merozoites

Plasmodium malaria parasites are obligate intracellular protozoans that use a unique form of locomotion, termed gliding motility, to move through host tissues and invade cells. The process is substrate dependent and powered by an actomyosin motor that drives the posterior translocation of extracellular adhesins which, in turn, propel the parasite forward. Gliding motility is essential for tissue translocation in the sporozoite and ookinete stages; however, the short-lived erythrocyte-invading merozoite stage has never been observed to undergo gliding movement. Here we show Plasmodium merozoites possess the ability to undergo gliding motility in vitro and that this mechanism is likely an important precursor step for successful parasite invasion. We demonstrate that two human infective species, Plasmodium falciparum and Plasmodium knowlesi, have distinct merozoite motility profiles which may reflect distinct invasion strategies. Additionally, we develop and validate a higher throughput assay to evaluate the effects of genetic and pharmacological perturbations on both the molecular motor and the complex signaling cascade that regulates motility in merozoites. The discovery of merozoite motility provides a model to study the glideosome and adds a dimension for work aiming to develop treatments targeting the blood stage invasion pathways.

Helical inchworming: a novel translocation mechanism for a ring ATPase

Ring ATPases perform a variety of tasks in the cell. Their function involves complex communication and coordination among the often identical subunits. Translocases in this group are of particular interest as they involve both chemical and mechanical actions in their operation. We study the DNA packaging motor of bacteriophage φ29, and using single-molecule optical tweezers and single-particle cryo-electron microscopy, have discovered a novel translocation mechanism for a molecular motor.